Role of RNA secondary structure in emergence of compartment specific hepatitis B virus immune escape variants

Table 1 Comparison of nucleotides at phylogenetically informative sites of subgenotypes A1 and A2 in GenBank sequences and in sequences isolated from our study population

Nucleotide Position of the HBV genome1	Base present in reference GenBank sequences			Base in genotype A1 sequences isolated from serum/plasma2	Base in genotype A2 sequences isolated from PBL2
	Aa/A1 (Asia)	Aa/A1 (South Africa)	Ae/A2 (Europe/United States)
505	c	t	t	c	t
514	c	c	a	c	a
616	a	a	g	a	g
619	t	t	c	t	c

¹Nucleotide positions indicate distance from the unique EcoRI site in the HBV genome;

²Sequences isolated from our study population. HBV: Hepatitis B virus; PBL: Peripheral blood leukocyte.

Table 2 Comparison of the thermodynamic characteristics of the minimum free energy secondary structure predictions for subgenotypes A1 and A2 pgRNA

Features	Subgenotype A1	Subgenotype A2
Minimum free energy of the optimal secondary structure	-1052.10 kcal/mol	-1049.50 kcal/mol
Free energy of the thermodynamic ensemble	-1099.56 kcal/mol	-1098.93 kcal/mol
Minimum free energy of the centroid secondary structure	-722.20 kcal/mol	-679.21 kcal/mol
Ensemble diversity	863.25	954.99